When working on complex molecular visualizations, clarity matters. Whether you’re analyzing large biomolecular systems or creating compelling visual outputs for presentations or publications, the choice of color can dramatically impact how easily your audience interprets molecular structures.
One of the recurring challenges molecular modelers face is differentiating molecular entities—be it residues, chains, secondary structures, or even arbitrary selections. For this, discrete color palettes are especially useful, as they assign clearly distinguishable colors to different items, avoiding overlap and confusion.
In SAMSON, a wide range of discrete color palettes are available by default to help you visually distinguish molecular groups. In this post, we’ll explore the discrete palettes provided and share some practical tips to help you choose the right one depending on your specific visualization needs.
What Are Discrete Color Palettes?
Unlike sequential palettes (which are ideal for gradient-based data like temperature or probability), discrete palettes assign distinct, contrasting colors to different categories. This makes them particularly useful when you need to highlight qualitative differences—such as different ligands, domains, or atom types.
Here’s an example of a popular discrete palette in SAMSON:
“Carto Pastel” is bright, soft, and offers subtle categorizations while preserving differentiation between components. It’s great for visualizing systems where visual harmony is preferred without losing category distinction.
Available Discrete Palettes in SAMSON
SAMSON includes over a dozen discrete palettes. Some highlights:
- Carto Vivid: High contrast colors for components that must be easily seen
- Okabe-Ito: Designed for colorblind-friendliness and print-safe design
- Accent, Paired, Set1–Set3: Classical color palettes used in many scientific contexts
- tab10, tab20, tab20b/c: Great for visualizing up to 20 distinct categories cleanly
- R4 and Dark2: Ideal for structural clarity in dense models
Here’s a glance at a few of these palettes side by side:
How to Choose?
- For clarity in crowded scenes: Use vivid or high contrast palettes like “Carto Vivid” or “tab20”.
- For accessibility: “Okabe-Ito” is designed to be distinguishable by people with color vision deficiency.
- For publication-friendly outputs: Choose softer palettes like “Carto Pastel” or “Set3” to reduce visual fatigue.
You can access these palettes through the Color Palette or Color Scheme dialog in SAMSON. You can even revert the arms of divergent palettes or create your own custom palette for specific contexts.
Choosing an appropriate color palette isn’t about aesthetics alone—it improves communication, guides attention, and reduces misinterpretation. The added flexibility in SAMSON ensures that your models look exactly as you need them.
To learn more about the available color palettes and how to customize your visualizations, visit the official documentation:
https://documentation.samson-connect.net/users/latest/color-palettes/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.